Gut microbiome of ancient Japanese people revealed with DNA

Ancient DNA extracted from fossilised poo has yielded clues about the inhabitants of Neolithic Japan’s gut microbiomes.

A team of Japanese scientists analysed coprolites (fossilised faeces) from the Early Jomon period, about 7,000-5,500 years ago.

They’ve been able to sequence a number of virus, microbe, and food genomes preserved in the coprolites, allowing them to learn more about the gut microbiome of the Jomon people.

The researchers have published their findings in PLOS One.

“As the microbes in the body have been highlighted playing roles in the health and disease of individuals, analyses of ancient microbial genomes could provide indicators of lifestyles, such as hunter–gathering or farming, and pathogenic states,” they write in their paper.

The samples came from a trove of more than 400 coprolites, excavated from a shell mound site in Fukui Prefecture during the 1970s.

This shell mound was a remnant of the Jomon people, who inhabited the Japanese archipelago from 16,000-2,900 years ago, according to the researchers. The coprolites used by the researchers came from layers in the mound estimated to be 7,000-5,500 years old.

The researchers sampled 10 to see which would have more DNA to analyse, then performed detailed genetic sequencing on 4 of those samples.

They used a method called “shotgun sequencing” to extract and collect genetic information.

Phylogenetic tree
Phylogenetic trees of detected gut bacteria in the coprolites. The researchers mapped 4,616 bacterial species. Credit: Nishimura et al., 2024, PLOS ONE, CC-BY 4.0

The results gave them a huge list of DNA from different organisms, mostly in small fragments. Much of the DNA came from viruses – especially phages, which are viruses that infect bacteria. The researchers also collected information on bacteria, fungi and microbes that lived in the people’s guts.

Some of the DNA probably came from foods the people had been eating, like salmon.

“Even though the average length of the reads was too short to analyse genomic variations, we still observed a vast number of reads mapped to the genomes of viruses, bacteria, and likely foods,” write the researchers in their paper.

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